Our Own Magic
by Savannah Runes
Summary: Edward and Alphonse Elric are mysteries wrapped in Shadowhunter gear and molten-gold eyes. When they turn up at the New York Institute, bloody and beaten up, everyone learns something new, maybe about love or friendship or maybe even about alchemy, which, as Ed so eloquently points out, is a fucking science, okay?
1. Poison

**A/N: This was written as prompt for the Downworlders Network Battles on tumblr (the prompt was crossover, Shadowhunter Chronicles and another fandom) and it totally ran away with me oops. I didn't mean for it to be so long, and this is only part one, which is really just introducing the characters omg. I reckon it will have about three parts but idk yet**

 **This is a Mortal Instruments and Fullmetal Alchemist crossover, but I reckon it can be read without knowledge of fma tbh, as it's set in the tmi universe and I've changed and explained all the characters and things that I've brought in from fma**  
 **(it contains royed too oh god i'm such trash)**

* * *

It all started when two strange boys showed up at the Institute.

Things had been settled since they had returned from Idris after defeating Sebastian, and for once shadowhunting duties had been going about as normal. Isabelle had been having a hard time adjusting to this new Simon, a Simon who was still trying to piece together the Shadow World and his role in it, but she was trying as well to accept him as he was now, and not lingering on the past, because there was nothing she could do about it now. Alec had finally packed up his things and moved in with Magnus, but he was still at the Institute virtually every day. But things had finally settled into something of a routine, something normal, or normal enough for the shadowhunters of New York.

But then one day, two strangers tumbled out of the elevator, bloody and bruised. They were both blond, and had similar facial features, which led Isabelle to immediately think that they were brothers. The taller one was carrying the shorter one in his arms since he was unconscious, his breathing shallow. There was a nasty cut on his left shoulder, blood oozing out lazily yet fatally. There was a stench in the air, something familiar and awful, reminding her of one of the worst days of her life: the day Alec had been poisoned. The short boy with the long hair tied back in a braid had been poisoned by a demon, and a powerful one by the looks of him. He was fading quickly, his skin pale and dull as he hung limply in his brothers arms.

At first she was so shocked to see these two seemingly mundane strangers having found their way into the Institute with wounds as serious as demon poisoning. They had no obvious runes on them that she could see so she doubted they were Shadowhunters, and they had no obvious markings of a Downworlder, though she wouldn't rule out the possibility. But all she could do was stand and gape as the short haired boy hauled his brother into the corridor, trailing a deep red colour along the floor.

She wasn't sure what to do until she saw the boy's eyes. They were a rich golden colour, reminding her of Jace, but they were wide and frantic. They conveyed the utter panic and terror that the boy was feeling at that moment; he was petrified for his brother's life. He could see his brother's life bleeding out in front of him, knew that the poison was consuming him slowly, and he was petrified.

Isabelle knew that look, knew it well, because she had worn it that day, that day when Alec had been poisoned by Abbadon and she had thought that he was going to die.

"Please," the boy whispered. His voice was small, but confident still. It was not an American accent, British if anything, though there was something else mixed in there too. "Please, help him. Help us."

Without a word, Isabelle was helping him, picking up the smaller boy and then they were carrying him, and she was leading them towards the infirmary. She knew that was perhaps being a bit too spontaneous, that she should question them first and see who, and what, they were, but that would take too long. This boy needed help now, and after seeing the raw love and care his brother had for him, no matter who they turned out to be, Isabelle knew that she was going to help them. She was not going to let this boy die, and she certainly was not going to let his brother be devastated. She simply would not allow it, not with thoughts of her and Alec being in that position racing through her mind.

"Who are you? And what happened here?" Depending on how powerful the demon was, she knew that she might have to call for more help, probably from Magnus. Especially if she could not rune them, because she had very rarely had to treat mundanes or Downworlders before.

They were nearly at the infirmary when he answered. "I'm Alphonse Elric, and this is my older brother, Edward." He looked at her apprehensively, as if unsure whether to trust her, then down at his brother, before carrying on. "We're Shadowhunters," he seemed to blurt, flashing his voyance rune on his right hand in front of Isabelle's face. She frowned as she realised that the permanent rune given to all shadowhunters seemed to be the only one on his body. She realised something else: she'd thought that he was British before, but now she realised that his accent was unmistakeably from Idris.

Confused as she was, she wasn't going to start questioning it now. There were more important things to be worrying about. They reached the infirmary and laid Edward down on a bed just as Alphonse said, "We were attacked by a group of Moloch demons—"

Isabelle cut him off. "Moloch demons couldn't do something like this. Unless…unless you faced their leader."

Alphonse looked down at his brother on the bed. "I don't know for sure. And I don't care much. All I know is that he's hurt, that he's been poisoned. I didn't know what to do; I drew a couple of iratzes, but they didn't do much. And we've only just arrived in New York really, we still don't know many people here, so I panicked and then we ended up here."

Isabelle could only nod as she looked down to examine Edward. The entire sleeve of the left arm of his jacket had been shredded and ripped, and the wound on his shoulder was deep. She could see the hastily drawn iratzes that Alphonse had mentioned, but they were already fading.

"Shit," she muttered under her breath. "This is really bad. I'm going to have to call Magnus, there's not much that I can do with just runes."

"Magnus? As in Magnus Bane, the High Warlock of Brooklyn?"

Under any other circumstance, she would have grinned at him, but that didn't really seem appropriate. "The one and only. Look, I'm going to go and call him, I'll tell him it's urgent and that he better haul his ass here like immediately. And then I'm going to find Clary, I think she's in the training room with Jace, and see if she has any runes that will help. I'll be five minutes tops, but you should stay here with him."

Alphonse nodded, albeit looking a bit confused, and she brought out her phone as she started to walk out of the room.

"Wait!" he called out after her. She turned around to look at him, his molten gold eyes piercing her. "I don't even know your name."

This time she did flash him a grin, even though it was small and short. "It's Isabelle. Isabelle Lightwood."

* * *

Isabelle returned, true to her word, exactly five minutes later. She had a short red-haired girl in tow, with bright green eyes and a smattering of freckles across her face. This must be Clary, who Isabelle had mentioned before. And behind her, there was a tall blond boy, who Al could only assume to be Jace. His eyes were a striking golden colour, and Al held his breath as he wondered what that could mean. With such distinctive eyes, the same eyes as his and Ed's, there had to be some story behind them.

"Magnus is on his way," said Isabelle, her dark eyes steady and her voice unwavering. She had been so amazing and so kind; just thinking about it made his heart swell.

But he knew that it was far from over. Because Ed was still lying on the bed, his eyes still closed and his breathing shallow.

Clary took her stele out, and leant over Ed, drawing swirling runes near his gaping wound. Some of them were runes that he didn't recognise, which confused Al as eh had studied virtually all of the runes in the Grey Book when he was younger. He couldn't bring himself to question it too much, because all he could think of was Ed, and how he couldn't possibly die. He couldn't because he was _Ed,_ he was his big brother who had always been there to protect him, who would walk to the ends of the Earth just to make sure that Al was safe. Ed's presence always filled a room, and even when their life had turned to shit, he could always make Al smile. Al couldn't even bear the possibility of losing him.

But Clary's runes did seem to be doing something, as Al was fairly certain that Ed wasn't bleeding as horrifically as before.

And then the doors to Institute opened once more, and two more people stepped in. The man in the front was wearing a long black thing that resembled a cloak and ripped skinny jeans, along with an extremely high quantity of glitter. His skin was caramel coloured, and he was probably from somewhere in far-east Asia. His eyes were the most unusual feature of his face: they were green gold and with slit pupils like a cat's. An unmistakeable warlock mark. This must be Magnus Bane.

Behind him was someone who was even taller than Magnus, with pale skin and dark hair. His stand out feature was definitely his eyes, which were like blue lamps shining from his face. He was wearing a more sombre outfit of an unremarkable grey sweater and jeans. He looked quite a lot like Isabelle, and Al decided that they were probably siblings. He wondered absently if they were as close and him and Ed.

"Magnus, thank God," Isabelle sighed, and the genuineness behind her voice struck him yet again. They were all being so incredibly helpful, and Al was a bit overwhelmed by their kindness. They didn't know him or Ed, and yet they all seemed to care about whether Ed lived or not. Those kinds of people were the best sort.

Magnus looked at him briefly, their eyes meeting in a flash. His cat eyes were unnerving, but Al didn't dare look away. It was Magnus who broke his gaze, proceeding to look down at Ed. His eyes narrowed.

"Everyone get out," Magnus demanded, his voice cool and collected. "This is going to take a while, and it won't help to have all of you here distracting me."

He didn't want to leave, and getting up and moving away from Ed was real struggle. It was so hard, knowing that he was leaving Ed's life in the hands of a complete stranger. He knew that he had no choice, but it was difficult nevertheless.

He followed the rest of the gathered teenagers out of the room, leaving his brother's fate completely and totally with Magnus.

He couldn't help but wince as the door shut behind him.

* * *

The waiting was utterly unbearable, and the tension in the air was making Al cringe.

The four of them had convened in the library, which was a huge room filled to the brim with books. Despite the circumstances, Al couldn't help but admire the overflowing shelves, and the smell of old books that hung in the air. It had been a long time since he'd been in an Institute library, so he'd almost forgotten how beautiful seeing all these books in one space was.

Clary and Jace had introduced themselves to him properly, and the other boy who had come in with Magnus had introduced himself as Alec Lightwood. He was right with his assumption that he was Isabelle's brother.

He'd told them all his and Ed's names and not much else; he was far too tired and worried to even begin to explain anything to them, though he did notice Isabelle looking at his lack of runes sceptically.

After a moment's silence, Alec spoke again, his voice quiet and tentative. "I was poisoned by a demon once. A Greater Demon, Abbadon. And Magnus was the one who healed me. Your brother is in good hands, Alphonse."

Al didn't really know how to respond, other than nodding. "Thank you," he murmured, looking down. Knowing that Alec was living, breathing proof that Ed had a chance comforted him, and made him feel a little bit lighter.

The thought hit him like a tonne of bricks after another few minutes of awkward silence.

"Shit," Al cursed, the violence of it surprising even himself. He was not usually one to swear: he had Ed for all that, but the word tumbled out of his lips anyway. "Shit, I need to call Roy."

He had four pairs of curious eyes on him, but he barely noticed. He was already taking out his mobile and finding Roy's number, his legs taking him out of the room and out of earshot of the other shadowhunters.

Thankfully, none of them followed him. He hit call as he found an empty room and waited with his breath held for Roy to answer. Phones didn't work in Alicante, but Roy lived just outside the glass city, and Al could only hope that he would be at his house. He didn't think he'd ever actually called Roy before, though he had heard him and Ed on the phone many times.

There were a few rings, during which Al's heart pounded in his chest, before Roy picked up.

"Ed, I do hope you realise it's two in the morning here." Roy's voice was deep and teasing, and Al got the feeling that Roy wouldn't actually mind if Ed woke him up just to talk. He also wasn't surprised that he assumed that it was Ed calling, but Roy's obliviousness made his chest hurt a little.

"Roy, it's Alphonse. I'm sorry for waking you, but it's an emergency. Brother's been hurt, we were attacked by a group of demons, and I think we may have faced a Greater Demon, I'm not really sure but it was going for me and then all of a sudden Ed was in front of me and he got hurt really bad. Demon poisoning. I panicked so I brought him to the New York Institute, but he was unconscious and bleeding everywhere and now he's in the infirmary with a warlock who's apparently healing him but—"

He was rambling and he was aware of it, but all the anxiety and worry and guilt he'd been feeling seemed to spill out. Talking to Roy wasn't like talking to the strangers of the Institute, nice as they were. Roy was someone who Al had known since he was eleven, someone who he'd admired growing up, and someone who cared about Ed completely. Someone, the only person really, who might love Ed as much as Al did.

"Fuck," Roy spat, and Al could hear ruffling sounds and crashes from the other end of the phone. He could envision Roy getting out of bed, his dark hair sticking up and his eyes wild. He could hear the worry and concern he had for Ed, even in that one curse. "Fuck, Al, he's gonna be alright. I'm gonna find someone who'll make me a portal or something, and I'm gonna get there as soon as I fucking can, okay? And if he wakes up before I get there, you tell him that I'm coming."

Al nodded, then stupidly realised that Roy couldn't see him, so quickly rectified it by saying, "Of course. I was so scared, Roy. That he was going to—"

"Stop there, Al, you know it won't do any good. He'll be fine, he's Edward fucking Elric, he's been through worse shit than this and you know it. I'll be there as soon as I can."

He was right, and Al knew he was right. Ed would be fine, he had to be. "Okay." It came out as barely more than a whisper. There were tears on his cheeks, and he didn't even know when they'd leaked out. Had it been during his conversation with Roy, or before? "Okay, we'll see you soon."

With that, he hung up.

* * *

When Alphonse came back into the library, his golden eyes were red and puffy, as if he had been crying a little. Clary couldn't help but feel for him. His brother had very nearly died, and his life was totally in the hands of a complete stranger, she would be surprised if he didn't shed a tear or two.

After Alphonse had found a seat, Clary was about to open her mouth and ask if he was alright, but Jace got there before her.

"So, who's Roy?" Sometimes her boyfriend was really dense when it came to things like this. Alphonse looked more like he needed a hug than prying questions.

"Jace," she scolded, whacking his arm lightly. "Stop being so nosy."

He shot her a look that seemed to say, _What?_ She glared at him until it turned at least a little sheepish.

"He's um, he's…" Alphonse seemed to be struggling for words. "He's a friend." She got the impression that there was a lot more to the story than that.

It was weird, because Alphonse and Edward looked like they could possibly be Jace's long lost relative or something, with eyes such an unusual hue of gold and glimmering, blond hair to match. Jace's golden eyes came from the blood of an angel running through his veins, and she couldn't help but wonder how they came about theirs.

The waiting after that was torturous. Clary had never even spoken a word to Edward Elric before, yet even she could feel anxiety swirling in the pit of her stomach. She couldn't imagine what Alphonse was feeling. She'd seen herself just how close Edward had been to the edge. He'd literally been hanging on for his dear life when Clary had come in. She could only hope that Magnus would do all he could to heal him.

Alphonse had taken to pacing, but she could see that it was only making him even more agitated. Finally, after a while, Alphonse said, "Do you mind if I look around at the books? It's been a long time since I've been in a library like this, and I wouldn't mind brushing up on some of my shadow world knowledge." The unspoken words were clear. He needed a distraction, desperately.

Clary sensed that the three Shadowhunters around her were a bit confused and curious about his statement, and she knew that there would be questions about it later. The whole circumstance of the Elrics was unusual: if they were Shadowhunters, why hadn't they come to stay or at the very least announce their presence to the Institute yet? And Clary was curious about the lack of runes and rune scars on his bare arms. Almost every shadowhunter she'd met had many runes all over their bodies, especially their arms. All that was on Alphonse's was the voyance rune and his brother's blood.

No one asked their questions then though, and Alec simply nodded as Alphonse went stalking through the shelves, his hands brushing along the spines of the old books.

When he was just out of ear shot, Isabelle began to speak. "I hope that this all turns out okay."

"I trust Magnus. I can understand why Alphonse is anxious, but we all know that Magnus won't let that boy die. And he's perfectly capable of doing something like this." Alec's voice was calm, but Clary figured that this whole thing was reminding him of the time when he himself had been poisoned like this. They couldn't be great memories to suddenly resurface.

There was a bit of silence, but then Isabelle cracked something of a smile. "That boy? You know, he does have a name, and besides, I think Edward is older than you, Alec. Didn't Alphonse say that he was eighteen? And Edward is his older brother."

Alec looked sceptical. "Really? He didn't look older than me…"

Alphonse appeared from behind a shelf, looking vaguely amused, which Clary supposed was better than the expression he'd had before. "You know, he'd probably kill you for that if he could hear you now. Ed has never been one to take jabs about his shortness lightly." Alphonse smiled fondly, as if imagining how Edward would react. His smile lit up his whole face, and was such a contrast to the pained expression he'd been wearing the whole time she'd known him.

He stalked off behind a shelf again, and the four members of the Institute were left with nothing to do but wonder what they had gotten themselves into.

* * *

After a while the waiting got a little easier, and conversation became a little less stilted between all of them. At one point they all got so hungry that Alec ordered pizza, although they had to move out of the library in order to eat it.

"Are you even allowed to order food to the Institute," Alphonse asked, halfway through a mouthful of his pizza.

Alec shrugged. He was growing more comfortable, yet also more intrigued with Alphonse and his brother by the second. "I don't even know, but our mom is away for the week for a Conclave meeting, so technically that means I'm in charge. And I'd rather order pizza than suffer through Isabelle's cooking again."

Isabelle grumbled from her place next to him. "I feel like my amazing cooking skills are being ridiculed far too often. Just because you can't appreciate my culinary genius—"

"Izzy," Jace cut in. "Whenever you take to the kitchen, even you can't stomach whatever you make afterwards."

All five of them shared a well needed laugh, and for a little while they could pretend that they were just normal teenagers hanging out and laughing. These were Alec's favourite moments, because they could just be friends without any of the weirdness and worry that came with shadowhunting. He wouldn't trade in being a Shadowhunter for the world, but sometimes it was nice to forget the burdens that came with that life.

Before they could finish their meal, someone burst into the room.

He was quite short, and oddly enough dressed in what Alec deduced to be pyjamas. His dark hair was ruffled, as if he'd just gotten out of bed, and his impossibly dark eyes were wild. The whole just-got-out-of-bed look was completed by the fact that he wasn't even wearing shoes, but navy blue slippers. He looked to be older, late twenties if Alec had to guess, but he couldn't say exactly. He had runes in various stages of fading swirling on his bare skin, and Alec could only assume that this was Roy, the person who Alphonse had called earlier.

Alphonse stood up a little awkwardly as probably-Roy entered the room.

"Angel, I forgot how big Institutes are. It took me fifteen minutes of wandering around this place to find you. I mean, I went to the infirmary first, of course, but promptly got kicked out by a guy who I hope is the warlock healing Ed, and then promptly got hopelessly lost. I'm just glad that I didn't end up wandering these corridors for the rest of my life."

"Ed would be disappointed if that were to happen." Alphonse gave the dark haired man a smile. "I'm glad you managed to get here so quickly, Roy. He'll be so happy to see you when he wakes up. It's been far too long since he's seen you."

Roy nodded, and then sat down next to Alphonse, who also took his seat. He could probably feel all the eyes in the room on him, because he said, "What? Okay yes, my attire is not at its greatest, but it's about 2:30am in Idris, and I didn't exactly have time to pick out my most dashing suit or anything." He looked around at all of them. "So, I'm guessing you're all residents of the Institute?"

Alec nodded and introduced all of them to Roy. "And you're Roy…?"

"Mustang. Roy Mustang."

"Hey, I've heard of you!" Isabelle said, almost excitedly. "You put your name forward for the position of Consul after Malachi died."

"I'm surprised anyone even knows or remembers. But yes, I did. It's always been my dream to become Consul, but I have no regrets about losing out to Jia. She makes a great Consul, and I suppose that someone like her, who's a little more experienced than me, was better suited to the job at the time. Isn't your father Inquisitor now?"

The sour look that must have passed across his face probably said more than words could about his precarious relationship with his father, because Roy didn't press the topic when nobody answered. Robert may have opened up a little at Jocelyn's wedding, but it was only the first step to mending his relationship with Alec, and both of them had known it. He hadn't even seen his father since then.

Alec wondered why someone like Roy, who he now vaguely remembered seeing in Clave meetings and around Alicante, had bothered to somehow come all the way to New York in the middle of the night. He couldn't help but wonder what the relationship between Edward and Roy really was.

"I hope he's alright," Roy whispered, almost to himself.

Alphonse sighed. "Me too."

A sadness and worry hung in the room. Seeing both of these people so worried about someone they cared about, someone who was in virtually the exact same position as he had been a few months ago, made Alec wonder if Izzy and Jace had been like this when he had been poisoned. He knew that they had been worried, but some part of him hoped that it had been like this, because it was so painstakingly obvious how much both Roy and Alphonse cared about Edward. It was etched all over their faces.

The conversation had turned awkward again, all their minds having been reminded of Edward and his condition pretty quickly.

And then, with no warning, Magnus appeared in the doorway. Alec's heart leapt at the sight of his boyfriend, who looked worn out and tired. Alec had to fight down the urge to wrap his arms round the warlock and kiss him.

"Is he okay?" Alphonse's voice was quick and hopeful. His golden eyes were shining.

Magnus nodded, and it was like the entire room let out a breath it hadn't known it was holding. Alec was certainly surprised about the relief that swept through him for a boy he hadn't even met before. Alphonse and Roy's anxiety had apparently been infectious.

"He's still asleep, but I don't know how long for. He'll be fine though."

Alphonse and Roy were both gone after that, their love for Edward, in whatever way that might be, making Alec smile a little as he watched their backs run towards the infirmary.

* * *

 **A/N: I'm sorry if the characters seem ooc, especially Al and Roy, but I guess that their worry for Ed is making them a bit different ahah and also they've had slightly different experiences than in canon haha**

 **Also i am aware Elric and Mustang aren't Shadowhunter names, but I can't help that**


	2. Mystery

Edward was still asleep, but he seemed to be actually asleep this time as opposed to unconscious and on the verge of death. His breathing was finally regular, and Magnus had cleaned up all the blood and put him in a new shirt, which was long sleeved and covered the wound he'd sustained. He looked peaceful.

He was actually a lot more beautiful than Isabelle had realised before. In the flurry of blood and panic, she hadn't had time to appreciate the soft curve of his jaw or the way his hair framed his face like spun gold. Along with Alphonse, it seemed that the Elrics had been blessed with particularly good genetics.

Alphonse and Roy appeared to have immediately taken up their positions beside Edward's bed. They both had expressions of relief and adoration on their faces, and Isabelle could see that they both cared about Edward immensely. She wondered what the relationship between Roy and Edward was; he was clearly important to Roy as he'd got up in the middle of the night and came all the way to New York the minute he'd heard he was injured. He was the first person Alphonse had called, and the way he was looking at Edward made her cheeks burn a little.

Magnus had looked shattered when he'd staggered in, and him and her brother were talking quietly in a corner, their faces close and their hands entwined. It made her smile that they'd managed to rekindle their relationship. Alec was so much happier when he was around Magnus, and Isabelle could tell that her brother was good for the warlock too. They'd both been miserable in their time apart, and she was so glad to see the smile back on Alec's face.

She was standing with Clary and Jace, talking casually. They were all waiting for Edward to wake up, but they didn't want to crowd around him. It would be better to see the familiar faces of Alphonse and Roy first.

The day was just beginning to fade when Edward Elric finally opened his eyes, which were just as brilliantly golden as his brother's.

"Ed!" Alphonse exclaimed, his smile radiant. "You're awake!"

Edward sat up with a groan, his unbraided hair falling past his shoulders. "Way to state the obvious Al," he muttered, his voice hoarse. His smile betrayed him though, because despite his seemingly annoyed words, he was grinning at his brother. Alphonse immediately enveloped him into a hug, and Isabelle could see the smiles and laughter on both of their faces.

And then Edward's eyes fell upon Roy. "You're here," he whispered.

"Well, yeah, I mean, you nearly died, Ed. I couldn't not be here."

They shared a gaze, which was intense and full of unspoken words. And then Edward cracked a smile, and Roy did too. "Bastard," said Edward, but he was grinning. It felt like more of an endearing nickname than an insult. "I missed you."

Roy said something else that was too quiet for her to hear from where she was standing, and then Roy and Edward collided, embracing so tightly that Isabelle could barely separate them. When their lips found each other's, she looked away. She felt like she was intruding on a private moment by looking. Though it confirmed her suspicions; it was clear Edward and Roy were a lot more than just friends.

When they finally pulled apart, the happy reunion was clearly over. Edward glanced around, taking in his surroundings for the first time. He saw the gathered Shadowhunters and Magnus, who'd moved to join them with Alec after Edward had woken up, and cursed rather profanely.

"We're at the fucking Institute?" Edward sounded a little surprised, and a little angry, for some reason.

Alphonse cringed a little, but stood his ground. "We didn't have a choice. You were dying, Ed, and we had nowhere to go, no one else who would help us. You would have done the same thing."

 _So they're Shadowhunters who don't like the Institute and don't wear runes. Just what is their story?_ Isabelle's curiosity was growing by the second. Her pile of questions was growing, and she kept having to remind herself that now was not the appropriate time.

Edward scowled and opened his mouth to speak, but Alphonse cut him off. "And before you start badmouthing any of them or this situation, they've done so much to help you. You would be _dead_ without their help. So you better be grateful, even though they're Shadowhunters."

The question was on the tip of her tongue, but Jace with his big mouth got there first. "What have you got against Shadowhunters, anyway? I thought you _were_ Shadowhunters."

Edward looked at their little group properly for the first time, then muttered, "Technically, we're Nephilim. We were born with the blood of the Angel running through our veins, and we're trained as Shadowhunters. But we no longer associate with the Clave."

"So you're running from the Clave? That's why you don't like being in the Institute?" She wanted to know their stories, to understand them better. All three of them had secrets in their eyes, and she couldn't help but wonder what they were.

"Sort of," Alphonse answered. "It's kind of a combination of running and being kicked out. The Clave made it clear that they disapproved of us."

All of them must have expressions of equal confusion on their faces, because Edward cut in. "Look, it's a really long story, which I am in no mood to relive right now. I feel like shit enough as it is, maybe we can recount our depressing life story for you some other time."

Silence settled in the room, only broken by Magnus. "Maybe we should leave them to it."

* * *

Edward was dismissed from the infirmary two days later, and none of them had tried to pry again. They'd all struck up something of a friendship, though Edward still looked warily at their runes when he thought they weren't looking.

Clary had almost expected them to leave as soon as they could, but they'd announced that they may as well stay for at least a few more days. "You said your mum wasn't returning until next week? Well, we can stay until then. We've not set foot in an Institute or anything for three years, so we may as well make the most of it while we can," Alphonse had said, his voice bright and his smile wide.

She was wandering down the labyrinthine halls of the Institute, vaguely heading to the training room. She'd thrown herself fully into her Shadowhunter training ever since getting back from Idris, and she could see the progress she had been making. To think that only a few months ago, she didn't even know that Shadowhunters existed was a crazy thought; she now lived her life immersed in the Shadow World.

She heard voices coming from the training room, and not the familiar voices of Jace or Alec or Izzy. The door was slightly ajar, and she peered in, curious as to who exactly was in there, and what they were doing.

"I seriously don't think you should be sparring, Ed. You've literally just gotten out of the infirmary, and you're already looking for a fight?"

Roy's voice floated through the air, but Clary barely heard them. She was too stunned by Edward and his arm.

She hadn't noticed before, but she hadn't actually seen Ed's right arm; it had always been covered. But now he was wearing just a white vest top, and his arms were completely exposed. The left one was bruised and scarred, but still definitely flesh and blood.

His right arm however, was made completely of metal. It was not like any prosthetic Clary had ever seen before, this looked like any normal arm except made entirely of metal. It attached to Edward at the shoulder and she could just about see the complicated mechanics that lay underneath it. There was a distinct, silvery tint to the metal that led Clary to suspect that there was some _adamas_ interwoven in the prosthetic.

It was odd, but Clary had to fight the urge to run and get her pad and pencils. The arm gave Ed such a unique and aesthetically intriguing quality; it contrasted heavily with the rest of him, which was very much human.

Though she knew that the circumstances under which he lost his arm must have been excruciating, she couldn't help but think that it was breathtakingly beautiful.

Edward flexed his metal fingers completely naturally, as though this was the arm he'd had his entire life. The metal had such life in it, and she found herself staring. Neither of them had noticed her peering through the door with her mouth open though, thankfully.

"I always spar after getting my arm repaired, and automail recovery is surprisingly more painful than demon poisoning recovery. Though the actual demon poisoning was a lot worse. But anyway, it helps me reaffirm my strength."

Roy rolled his eyes, but he seemed to have accepted the fact that Edward wasn't going to budge. Somewhere in the back of her mind, she knew that she should probably intervene: Ed shouldn't be sparring under any circumstances, but she was too transfixed. And she knew that Roy wasn't going to hurt Edward.

"I usually spar Al, but I figure I have a bigger chance of beating you than him." Ed smiled smugly.

Roy's smile, however, was equally as sly. "You don't stand a chance, and you know it."

Edward grinned at his boyfriend (at least Clary assumed that they were together. They hadn't kissed publicly since just after Ed woke up, and they hadn't talked about their relationship either). He lifted his hands, as if about to clap, which seemed a little odd. His right arm moved just as fluidly as his left, the metal moving seamlessly and silently.

"Uhuh," Roy tutted. "No alchemy."

 _Alchemy? What the hell's alchemy? It sounds like some black magic crap mundanes would try on Halloween or something._ Clary's thoughts raced, and she wondered if this alchemy was part of the reason the Clave had kicked out the Elric brothers.

"Hey, that's not fair." Edward moved his hands back down to his sides. "You know that alchemy is my strong point in fights."

"We're in an enclosed space, in an Institute for god's sake. It wouldn't be good manners to completely wreck the training room."

"Fine," Ed muttered, seemingly a little pissed off about Roy's rule, but prepared to fight anyway.

"Hey Clary, what are you—" Alphonse's cheerful voice came from behind her, and she nearly jumped out her skin.

The two men in the training room both looked at the door, where she now stood rather awkwardly, her face gradually turning the colour of her hair. She felt like a character from a movie, and finally understood why it was so mortifying to be caught eavesdropping.

Alphonse, who stood behind her, seemed to realise what his brother had been about to do, because before she could try and explain herself, he cut in.

"Ed, what in the Angel's name do you think you're doing? You should be resting, not sparring."

Alphonse's golden eyes were livid, his tone of voice even more so.

"I've been resting for two days, Al. And besides, you are always happy to spar with me after I get my arm repaired. How is this any different?"

"That's different and you know it. And besides, you've barely been out of bed for two hours, can't you find something a little less violent to do?"

"But—"

Alphonse shot him a glare, a glare that Clary was glad she wasn't on the receiving end of. She had never imagined that Alphonse could be scary at all; he seemed so gentle. But she decided that Alphonse Elric was definitely the scarier of the two brothers when he wanted to be.

"No," Al said, and it seemed that was final. Edward looked resigned and a little dejected, but didn't say anything else.

"So Clary," Roy's deep voice brought her back to the awkward situation she had almost forgotten she was in. "What were you doing?"

"Um," she stuttered. "I was just passing, and…" She wanted to say something about Ed's arm, but that was just embarrassing, so instead she found herself blurting out, "What's alchemy?"

A look was shared between the three men, communicating something that she couldn't place.

"So you were eavesdropping?" asked Roy, and she blushed even more than before.

"It was an accident, I swear," she stammered.

He gave her a look, as if to say ' _Sure it was',_ but luckily didn't press the subject.

"Alchemy is…complicated," said Edward, his arm glinting in the sunlight that filtered through the windows. "It's basically the reason the Clave hate us."

Ed looked so furious all of a sudden, just thinking about it making him angry. He clenched and unclenched both of his fists, the fake one moving just as perfectly as the real one.

"It sounds like some sort of magic." Her voice was small, timid. She didn't want to press the subject too hard, but her curiosity got the better of her. If this alchemy was really the thing that got them kicked out of the Clave, she couldn't imagine how dangerous it might be. She knew that Shadowhunters didn't have or use magic, they left that business to warlocks. If the Clave had found out that Ed and Al were actively doing magic, she could easily imagine why they would flee.

She didn't expect Edward's reaction to her little remark, however. "It's not magic!" Ed yelled, his voice raised. She almost took a step back at the fierceness of it, at the exasperation and fury behind the words.

"Brother," Alphonse exclaimed, clearly embarrassed by Edward's outburst. Clary got the feeling that he was constantly apologising about his brother's obviously short temper. "There's no need to get mad."

Ed looked at her, but she could tell that he wasn't really angry at her. The anger in his eyes was directed somewhere else, most likely at the Clave. "I'm not _mad,_ I'm just annoyed that everyone assumes it's magic before we explain it. I guess I'm just kind of eternally pissed off about the whole thing, to be honest."

"So am I," whispered Alphonse. "But you that doesn't give you the right to blow your temper at Clary."

"I know." Edward looked down. "I'm sorry."

Somehow, she was more confused than before about the whole thing. Just what was alchemy, if it wasn't magic? What did it mean to Ed and Al, and Roy, who was clearly still a Clave member?

"It's alright. I'm just a bit lost. You never answered my original question, you know."

Again, that look passed between all three of them, leaving her on the outside. "We came to New York to seek out Magnus Bane," said Edward, knocking Clary off guard. She didn't have a clue how that was relevant; it certainly didn't answer her question. "It's funny how life works in a series of coincidences."

"What?" She sounded a little bewildered.

"As I said before, alchemy is complicated, and our story is too. I only really want to tell it once, but we need to tell it to Magnus. You and the rest of your little…gang can come with us, and we'll tell you too. I figure you all deserve it, for helping us so much."

* * *

Magnus Bane had had an odd few days, but really, all of his days are odd. In all his life, he had never had any semblance of normal, and he was totally fine with that.

A frantic phone call from Isabelle Lightwood saying that two mysterious Shadowhunters had turned up, one of them dying of demon poisoning, however, was surprising enough to be called odd even in his books. He couldn't say no, obviously, and so he found himself at the Institute, the whole situation reminding him of the time he'd healed Alec. It wasn't the greatest thing to be reminded of on a Monday afternoon.

The two Shadowhunters, Alphonse and Edward Elric, were familiar in a strange sort of way. He was almost positive he'd never met the before (he was sure he would remember _that,_ because damn those brothers were certainly beautiful). Maybe he'd met a relative of theirs at some point, some ancestor or something.

After he'd dismissed Edward from the infirmary, and Magnus had not been able to shake off his curiosity about the Elric brothers, and their dark haired companion who was so obviously in love with Edward. It seemed that his curiosity was shared by the rest of the Nephilim at the Institute, but Alec had said that they hadn't revealed any more personal information, and only talked about safe topics around them.

Alec had been worried about the whole thing, in a totally Alec way. He was currently standing in for his mother as head of the Institute, and the unexpected arrival of three new Shadowhunters was making him panic a little. "Should I tell my mom? I mean, she'd probably want to know. But they're runaways from the Clave, and it's clear that they don't want the Clave to know they're staying in an Institute. Obviously I can't kick them out, and they seem really sincere, especially that Alphonse, but what if—"

He had been cut off by Magnus pressing their lips together, amused but having had enough of Alec's rambling. He had felt Alec relax under him and he'd smiled into the kiss.

"Stop worrying, my Alec. You're doing the right thing by letting them stay, and if they don't want the Clave to know they're here you should respect that. You know how the Clave can be with this sort of thing. They're not dangerous, so you're allowed to relax about it."

Alec had smiled a little, and god Magnus loved it when Alec smiled. His blue eyes turned so bright, and his mouth crinkled in the most adorable way. He hadn't even realised how much he missed things like Alec's smile until they were gone. Since he'd taken Magnus back, he'd been resolved to make Alec smile as much as he could, because he fell a little bit more in love every time.

"You're right, of course." He had tugged the end of his sweater over his hand, and Magnus could see the fraying edge where he'd been messing with the sleeve when he was nervous. "It's just…we know so little about them. They must realise that being all brooding and aloof is making all of us die of an intense desire to know their life story. The less we know, the more we want to."

"That is a feeling that I know I can relate to."

That had been two days ago, and Magnus was now curled up on his couch with Chairman Meow, his boyfriend making coffee in the kitchen. He never knew someone could drink so much coffee until he met Alexander Lightwood, who seemed to require at least three cups a day. The coffee machine had turned out to be the most valuable addition to his apartment in years.

The TV was on, but Magnus wasn't paying much attention. His mind was wandering, and he was stroking Chairman Meow absentmindedly, waiting for Alec to return.

The buzzer startled him; he wasn't expecting any more clients today. Alec came out of the kitchen with his mug of coffee in hand, shrugging when Magnus asked him if he knew who was at the door.

"Who dares disturb the High Warlock?" He could hear Alec snort from behind him. The rather intimidating greeting had become a customary routine every time someone buzzed when Alec was around, and it had led to some hilarious situations with delivery guys.

"Magnus, it's us," said Isabelle's voice through the speaker. He buzzed to let her and whoever 'us' meant, wondering if it included the Elrics and Mustang.

It appears it did, because the next thing he knew, his apartment was filled with all the current residents of the Institute. It was far from the lazy afternoon he'd thought he'd be spending with Alec, but it had definitely become interesting.

They settled around the table: it was the only thing big enough to accommodate all eight of them. Next to him, Alec took a sip of his drink, before realising his manners and offering everyone else one. Everyone refused, except Roy, who asked for water, and Alphonse, who asked for a glass of milk. This, for some reason, earned him a glare from Edward, and a laugh from Roy.

"So, to what do I owe the pleasure?"

* * *

 **A/N: Next chapter: finally explaining about alchemy and their story.**

 **I predict one or two more chapters of this, idk we'll have to see (the characters probably seem so ooc in this oh my god, oh well. and we got some cute malec scenes, which is always good)**


	3. Alchemy

**A/N: Hey guys! I finally finished this chapter, I hope you like it! There's a lot of explanations and stuff, but I tried to make it as interesting as I could. I think there will be one more chapter after this now.**

 **Please let me know what you thought, and I'm sorry for the huge wait**

* * *

Before anything, Ed knew that he had to thank Magnus for healing him. He hadn't really seen the warlock since the day when he'd been injured, and he now owed his life to him. It was odd to have Magnus just wave it off, as if he did things like heal someone from Greater Demon poisoning every day. Though the life of a warlock must be full of surprises like that.

And then it came to his promise to Clary: that he would explain alchemy and their story to them. They had all been so amazing, and despite the fact that they were Shadowhunters, Ed felt a weird desire to tell them about it.

Ed wasn't entirely sure why though, but sitting at the table across from four Shadowhunters and one warlock with expectations in their eyes was slightly intimidating. He absently wondered why he'd ever promised Clary that they would explain anything, because now that it actually came to it, the words seemed to be stuck in his throat.

"So…our life story. Where to begin?" He was pretty sure that just sounded random and awkward, but he couldn't formulate the words to explain everything.

Everyone was looking at him oddly, and Ed was silently grateful when Al took over for him.

"I guess we should start with Xerxes."

"Isn't Xerxes that guy from Persia or something?" asked Magnus.

"Sure, but it was also a place. Thousands of years ago, there was an ancient desert civilisation of the same name. We don't really know where it was, or much about it really, but the Xerxians developed the art of alchemy."

Ed looked around at the table, but the Shadowhunters' faces were blank at the mention of the word that had changed Ed's life. Magnus's eyebrows, on the other hand, quirked up a little, and he became visibly more intrigued, though he didn't say anything.

Ed finally found his voice, and interjected. "The reason we don't know much about Xerxes is because the entire population was wiped out in one night. Our dad, Van Hohenheim, was the only survivor, so he was the only one preserved the knowledge of Xerxes and of the alchemy which was developed there."

Alec held a hand up. "Wait, your _dad?_ I thought you said this Xerxes or whatever got wiped out thousands of years ago."

At virtually the same time, Magnus said, "Van Hohenheim?"

"Yes and yes." Ed was definitely surprised at the recognition that resonated in Magnus's eyes as he mentioned Hohenheim's name. "Have you heard of him, Magnus?"

Magnus nodded, looking a little confused. "I've met him. But that must have been over two hundred years ago."

Ed couldn't help but let out a little sigh, and an almost derisive laugh. "Of course you have. Is there anyone the bastard hasn't met, anything he hasn't done?"

"Brother," Al scolded. "Don't use that language to describe dad."

Ed scowled, because he still hadn't fully forgiven Hohenheim for leaving the two of them and their mum alone when they were young. He had accepted that Hohenheim had done what he'd done to save people, but the fact he'd spent his childhood without his dad, who could've helped with the disaster that had cost him his arm left Ed with a bitter taste in his mouth.

Magnus's cat eyes were intrigued as he stared at Ed and his brother, reclining slowly into his chair. "I assumed that he was a warlock, he could do something I presumed to be magic and mentioned his immortality. But clearly that's not the case, looking at you." He gestured his ringed fingers at the two of them. "I knew that you looked familiar."

Al and Ed shared a quick glance, and then Al said, "He was immortal, sure, but that only came as a consequence of the alchemical ritual that destroyed Xerxes. It's a little complicated, but he became a sort of living philosopher's stone…"

"What's that?" Isabelle interrupted, curiosity burning in her dark eyes.

There were too many questions, and no easy way to go about explaining it all. Thinking about all the things that were all so interconnected, actually facing their lives and trying to explain it was tougher than Ed had anticipated.

He looked to Roy for help; he was a politician, or at least some form of it, and he probably knew how to explain things better than Ed did.

"Maybe it would be better to explain what alchemy actually is first, before going into things like the philosopher's stone." As always, though Ed admitted it begrudgingly, Roy's advice was infallible.

Taking a deep breath, Ed said, "Alchemy is essentially a science, based on the concept of equivalent exchange. The complex science behind it allows its users to manipulate substances into other forms, but in order to make something, something of equal value must be given or used as you can't make something out of nothing."

The blank looks he got back weren't exactly inspiring. And that explanation barely even scratched on the surface of the complexity of alchemy.

Ed sighed. "Maybe it would be easier if I just showed you."

Ed raised his gloved hands and brought them together in the clapping motion that had become so familiar to him that it was second nature. As he drew them together, he created the circle, and then put his hands on the table to complete the transmutation.

From the table sprang a pole, as Ed wasn't feeling particularly creative. He was tempted to add a caricature of himself on the end, as he would have done when he was younger, though he managed to refrain. Just.

The Shadowhunters' eyes stared at the pole, complete with the transmutation marks, in complete wonder. They looked from Ed to his hands, and back at the transmuted pole, leaving Ed feeling a little self-conscious. It wasn't like it was hugely complicated transmutation, though he knew that they must be surprised because they had simply never seen anyone do alchemy before.

"That should be impossible. You're a Shadowhunter, and Nephilim can't do magic," murmured Jace.

"Alchemy's not magic," said Ed adamantly. He had anticipated this, but it was still mildly annoying. "It's not, it's actually a science that simply involves being able to manipulate elements to create new things, it doesn't involve any spells or any of that crap."

"Hey, don't talk down on magic." Magnus was definitely intrigued now, as he was smiling at the three of them. "But you're right, alchemy isn't magic, so it's very rarely used within magic circles because we have no need for it. And the knowledge of it has dwindled over the years, I've only ever met about three people who have had any knowledge of it, one of them being your dad apparently."

Ed was curious about how and where Magnus had met Hohenheim, and what information his dad had divulged, especially about alchemy. Any information about alchemy really was quite precious to him. And the fact that Magnus seemingly had some knowledge of alchemy was extremely helpful when it came to what they had originally wanted to request from him.

"Our dad left us and our mum when we were children. He had Ascended, and had become a Shadowhunter so he could live in Idris with mum, but left abruptly when I was about two. The only thing he left behind were books upon books about alchemy."

Al carried on the story, picking up the flow from where Ed had left it. The advantage of being so close was that they had both learnt to read each other, and in circumstances like this Ed knew almost exactly what Al was going to say, and it was more than likely the same for Al too. "We were both curious children, and smart too. We lapped up our Shadowhunter training like it was nothing, always thirsting for more knowledge. Eventually we found our dad's old alchemy books, and taught it to ourselves. Anyone can learn it, mundane or Downworlder or Shadowhunter, if they have the right knowledge and understanding of it. It took us years to master it, but we loved the challenge, and we never really comprehended the consequences that it might bring."

"We saw it as another challenge to master, but somewhere along the way we both fell in love with the alchemy, with the science and the endless possibilities behind it. At least to us, it's genuinely fascinating, though I'm not sure if that applies to everyone."

From next to him, Roy shrugged. "I found it fascinating as well, you know. You don't have to make out that you're some sort of high almighty genius because you understood alchemy."

"Try mastering it when you're twelve and then come back and have this conversation." Roy grinned at him, his smile like the sun and Ed felt even lighter. Even just having Roy there next to him was infinite times more comforting, made him feel more at home. They may have been teasing each other, but with Roy that was the thing that came most naturally, the thing that had built their relationship into what it was now.

Alphonse coughed a little. "You two can go back to your flirting later," he said, which made Ed splutter a little. "Back to the topic at hand, basically we learnt alchemy as kids, and it was all great until our mum died when we were very young. We were devastated by her loss, and were also too young and foolish to really know what we were doing.

"We got taken in by the Academy in Idris originally, but we spent a lot of time with our dad's old friend, Izumi Curtis. She's a mundane, a great woman—"

"Scary as hell," muttered Ed under his breath, but his lips were quirked up in a small smile at the memory of their teacher."

"—well anyway, she knows alchemy, and she ended up teaching us a lot of it. So as we said before, even mundane a can learn it if they really want to."

Knowing where the story was inevitably taking them made Ed feel a little sick. He'd made such a huge mistake back then, and it had cost both him and Al so much that just thinking about it made him cringe. He may have reconciled with the consequences of his actions all those years ago, but he was still ashamed of them. His automail arm was a constant reminder of what he had done, and that was never going to go away.

"When I was about eleven, I came up with the great idea of using alchemy to try to bring our mum back from the dead." There was no way of making that sentence sound anything other than it was, no way of alleviating the painful memories that accompanied it.

The Shadowhunters' eyes widened at the thought of it. But there was also a sadness on all of their faces, a tell-tale sign of them having lost someone important to them. "Did—did it work?" Isabelle asked, her voice impossibly sad.

A lump formed in Ed's throat, though he wasn't entirely sure why. Perhaps it was the sadness on Isabelle's face, the way Alec's bright eyes looked downwards, endless pain behind them, or maybe it was simply the way that Roy's hand had found his under the table, squeezing it hard and acknowledging the pain that he had gone through.

"No," he whispered. "No, it didn't."

Silence descended on the room, pervasive and intrusive. It filled every crevice and for the first time, Ed realised that yes, his and Al's story involved pain and grief, but theirs wasn't the only one that did. These Shadowhunters before him had been part of two wars, and from what he had heard played fairly significant roles. They had seen death and had endured loss in equal, possibly surpassing, measures to him. Magnus, who had the composure that only an immortal could have, had seen even more shit than all of them combined.

They all told sad stories, because that was their lives, but maybe that wasn't the only thing they could share. The trust and love and family he had seen already between this group of Shadowhunters, this group of people who were part of a collective that he had grown to despise, was astounding, and they were actually were some of the truest, most honest and likeable people he had met in a long time. And he was hurting now because of their sadness, even though he had no idea what it entailed. It was an odd feeling, but Ed realised that it was somehow not entirely unwelcome.

Al was the one who broke the silence, and Ed was glad because he wasn't sure if he ever would have done. "Our attempt at human transmutation, which is a forbidden practice anyway, backfired on us hugely. It's a bit confusing, and honestly I'm not sure either of us want to go into it in any huge detail," he said softly, looking at Ed the entire time. "But since alchemy works heavily on the principle of equivalent exchange, we couldn't escape unscathed…"

Clary's green eyes widened, and Ed was hyper aware of her looking intensely at his right arm, which was currently covered by his jacket sleeve. He'd noticed how taken she had seemed with his automail; she'd almost been as bad as Winry with the look of wonder in her eyes.

"Your arm. That was the price, wasn't it? You lost your arm."

Ed could've hung his head in shame, but instead he tilted his chin up and didn't break any of their gazes. He'd never been one to be ashamed of his automail, especially since he knew that Winry would kill him if he was. "Yes." He took of his jacket and glove, leaving the metal exposed. He knew that it was a sight the first time, a mixture of steel and _adamas_ interwoven into a prosthetic that was almost as natural as the real thing. The love that Winry had poured into it was evident, and through it Ed was so proud of his mechanic friend, who was really more like a sister to him.

"That is so cool," breathed Jace, clearly admiring it. If Winry could see the appreciation of her handiwork Ed was almost guaranteed she would explode of excitement.

"Jace," Alec scolded. "He lost his _arm._ You can't just go around saying it's cool."

Jace pouted a little. "Well okay the losing the arm part is definitely not cool, but obviously I was talking about the arm itself. I've never seen a prosthetic so life like before. It's literally like your arm is just made of metal. You could probably do super awesome things with it like hide weapons or something."

Alec just rolled his eyes. "Only you would immediately jump to the possibility of hiding weapons."

Ed found himself grinning. "Don't give my mechanic any ideas, Jace. I can tell she'd get along great with you. And I don't hide weapons in it, mainly because I usually use alchemy to actually turn it into a weapon itself." Feeling the need for another demonstration, although it was possibly more of a need to show off, Ed clapped his hands again, and this time used the metal of his arm to create a blade jutting out from behind his knuckles. "Since our mechanic and best friend, Winry, already infused the automail with _adamas_ the need for a seraph blade is gone too."

Jace was practically hitting the roof with excitement at this point, and all the others were now a lot less sad and a lot more curious. "Angel, I almost want to lose my arm just so I can get one of these automail things."

It was Roy and Al's turn to roll their eyes now. "You can stop showing off you know, Edward," said Roy. "You're giving certain people wild ideas which are definitely not recommendable."

"True, automail is very badass," he started, which earned him an amused look from Roy, which he responded to by very maturely shoving the older man. "But the surgery and recovery hurts worse than hell. And for some reason mine is always breaking."

"That's because you're a reckless with it, brother," said Al. "I've never broken mine."

"Yeah, yeah, you don't need to show off, Al."

Clary looked curiously at Al. "You have automail too?"

Al stood up and lifted up the bottom of his trouser leg and revealed the metal leg underneath. "We both performed the transmutation, and we both paid the price for it."

That silence came again, a sudden reminder of everything. But it was quickly gone, the group of them determined to not let it beat them.

Jace smiled and said, "I still think the automail is awesome," and even though it was absurd, Ed smiled too. The mood lifted again just as quickly as it had dropped, which made Ed indescribably and oddly happy. He hadn't expected to sit around this table and feel as though he was among friends, but here he was, genuinely considering these Shadowhunters as friends.

"So, we know what alchemy is, kind of," said Isabelle. "But what about you, and your father and the Clave? Why are you on the run or whatever you're doing?"

Ed and Al glanced at each other, giving each other loaded looks. Al began, "Again, it's a very long story. Our dad's story is too complex to go into now, really, but after an alchemical ritual, which he was coerced into, which used the lives of the Xerxians to turn him into a philosopher's stone, he became basically immortal. A philosopher's stone allows its user to bypass the laws of equivalent exchange and create something out of nothing whilst using alchemy."

Carrying on seamlessly from where Al had left off, Ed carried on. "Our mum, Trisha Elric, was born a Shadowhunter and met Hohenheim whilst out hunting demons. With being alive so long, and undoubtedly through meeting people like you, Magnus, he was aware of the Shadow World, but to marry her he still had to Ascend, because of course the logic of the Clave is flawless."

Briefly, he wondered whether he might offend any of the Shadowhunters by bashing the Clave so openly and sarcastically, but none of them batted an eyelash. He figured that they must have enough reasons already to criticise the Clave, undoubtedly after experiencing the wars that they had. And with Alec being openly gay and in a relationship with a Downworlder, he'd undoubtedly experienced some negative reactions. It made Ed admire Alec, as here he could see a man who was finally happy and comfortable with his friends and boyfriend and wasn't going to let the Clave rule that. Even if he wasn't on the run from the Clave, he would be hesitant to be open about his and Roy's relationship, so seeing Alec so happy made him feel a bit warm inside.

"He Ascended and we were born, but he left again so quickly, so we grew up in Idris in the countryside, learning about alchemy alongside out Shadowhunter training. After the disaster that was the human transmutation, and after we had been through our automail surgery and recovery, we decided to leave Idris as it brought back too many bad memories."

Ed thought involuntarily of the night they had left, of the flams that had consumed the life that he had once known in that house, the life of safeness and family and of the innocence of childhood. That innocence had been erased the night they had performed the transmutation, and the reminder of it was too much to bear. Now it was just ruins.

"Then there were the wild adventure years, which involved us starting off by searching for the philosopher's stone to try and right our wrongs, but ended up with us fighting off a group of people who were determined to take over the world. Their leader, who was actually the person who had forced our dad into the alchemical ritual, was called, very ominously, simply Father. I mean seriously you can't get more of a villainous name than _Father._ Not to mention the pretentiousness of it."

" _Brother,_ " said Al exasperatedly. "Stop divulging."

He shot Al a withering glare, but did carry on without saying anything else. "So Father wanted to basically take over the world and use the souls of Shadowhunters to turn himself into a god, and he had needed us as human sacrifices so we spent a good two or three years travelling from place to place, avoiding him and his lackeys. This was when we really started distancing ourselves from the Clave. We started staying with mundanes as opposed to at Institutes, started only fighting demons if they sought us out first. Having taken a step back from it, we could see all the flaws in the system, all the prejudices and cracks. We didn't want to stay in this toxic system where we felt a little uncomfortable. Not that we didn't believe in the Clave's ultimate mission, but we just couldn't agree with all the things they were doing."

The words laid heavily in the room, clearly weighing down on the four Shadowhunters. They might've acknowledged some of the Clave's flaws, but Ed could tell that hearing those words coming from Ed was still a shock to them. The fact that they were Nephilim and yet had chosen to leave the Clave not just forced out of it would definitely be shocking enough for them.

The tension in the room was almost tangible, and Ed was drowning in it.

But Roy squeezed his hand again, and then put on a light voice to diffuse the tension. "Those years weren't all bad, Ed. That was when you met me."

Ed smiled a little. "Yeah, back when you were a cocky training officer fresh out of the Academy who took pity on us or something."

"I didn't take pity on you. I saw the fire in your eyes, saw your fighting spirit."

Ed looked at Roy, who was looking at him with soft eyes and a small smile, and the love in his eyes made Ed's heart swell. It was still a fairly new sensation, having someone who was in love with him, and it overwhelmed him sometimes, though in the best possible way. He'd almost forgotten that there was anyone else in the room with the way Roy was looking at him.

He was jolted back into the room by Al picking up the story again. "Forgive their sappiness," he said, but he was smiling at the two of them, which just made the edges of Ed's cheeks burn. "Anyway, as my brother was saying before he got distracted, we were already distant from the Clave, but when Father took the fight to Idris and tried to wipe out all Shadowhunters, we were determined on bringing him down. We were by no means alone; we had so much help from others like Roy, and his parabatai Riza, and their friends who they'd trained with, and Winry and other friends we'd picked up along the way in our travels. And our dad, who we'd been estranged from for years, came back and ended up saving everyone."

Ed nodded. "We couldn't have defeated Father if it hadn't had been for the help we were given. Father tried to use the two of us and our dad and teacher as human sacrifices, and would've succeeded in using alchemy to kill all the Shadowhunters in Idris at the time if it weren't for Hohenheim, who'd spent all these years building a defence mechanism for when Father would try this, involving the souls that had been killed all the way back in Xerxes. To cut a long story short, Father was weakened a lot after what our dad had done, and in the final battle, we used our own alchemy and skills to fully defeat him, so he couldn't become a god and take over the world."

By now, everyone's mouths hang open slightly. "You saved the entire world, and we never even knew that it had been in danger in the first place," said Jace, a little numbly.

"Well, the only recognition we got from the Clave was horror. They jumped to the conclusion that we had dabbled in some sort of sorcery with demons or something when we made our alchemy public, and we were given a sort of ultimatum: to flee and never go back to Idris again, to the land we grew up, to where our mum is buried, and where our father lies at the crossroads, buried as a traitor after his alchemy was revealed. He didn't even get the privilege of being buried with the only woman he had loved. Or we could stay and face the consequences, undoubtedly ending up with our Marks being stripped."

This time the silence that fell was filled with a slow, simmering anger that had built up within Ed's little speech.

"So you fled," said Clary quietly.

"It was the only choice. But now we're ready to shake the Clave from its foundations, to reform the Nephilim into the race that they can truly be."


	4. Hope

**A/N: And we have reached the end! This is the first time I've actually finished a multi-chapter fic, so I'm kinda glad that I have. I hope that you all enjoyed this fic, it was so fun to combine two of my favourite things and explore this verse.**

 **Please let me know what you thought of this fic overall, and thank you for reading.**

* * *

A stunned silence hit the room like a tonne of bricks at Ed's words, and this bold and radical statement. Everyone was a little shocked; Ed could see it in their eyes.

"What my brother meant to say, despite his ridiculous, radical flair, was that we want to try and help the Clave with our knowledge," said Al, and sometimes Ed was reminded how thankful he was for having Al as a brother. He forgot what he was saying sometimes, but Al was always right there to pick everything up and to put it in the right words.

But he had meant what he'd said. "Kinda. I think reform was a better word for it, though."

Roy shook his head. "Of course you would."

The Shadowhunters were still in a bit of shock, so Magnus was the first one to speak. "So you want to use alchemy to change the stubborn views of the Clave?"

Ed nodded. "Obviously it's going to be slow and difficult. The Clave is stubborn as fuck, and we're not naïve enough to think that the two of us can do it alone. But we wouldn't be able to live without trying, and we both know that we have to do whatever we can."

"We were kicked out, essentially, for saving the Clave with our alchemy, but we can't just spend the rest of our lives bitter and complacent about it." Al agreed, and Ed could almost see the passion behind his brother's eyes. This had, of course, been Al's idea to begin with: to try and help rather than sit around, even though the odds were against them.

Next to him, Roy leaned back on his chair. "Yeah, only the Elric brothers would be as stubborn as the Clave and decide that they want to 'reform' it. Once they've got their minds set on something, they're not going to give up on it."

Clary was the first of the Shadowhunters to respond to this statement. "You know what? I'm kinda glad. The Clave is far from perfect, and what they did to you was unacceptable. You saved them, and they ran you out of your own community."

This shocked Ed; he hadn't been expecting such a positive response. But then again, Clary hadn't grown up as a Shadowhunter, and perhaps she wasn't as firmly hooked by the Clave as most Shadowhunters were.

Al, being his sugar sweet self, grinned at Clary. Ed could virtually see his eyes twinkling as though he was a cartoon character or something. "Why thank you, Clary. It's nice to know that we aren't the only Shadowhunters who think that some change is needed."

There was a small silence, and then, "The law is hard, but it is the law," murmured Alec. Ed knew that it was coming: these were all trained Shadowhunters, and they hadn't had the bad experiences they'd had with the Clave. From a young age all Shadowhunters are taught to be obedient soldiers, to follow the rules no matter what.

 _Sed lex dura lex_ had been instilled in him from such a young age that he himself had once believed it, before he had discovered the wonders of alchemy and began to realise that the rules were too hard to be followed sometimes. It was a long journey for him and Al to realise that the Clave weren't always right, and it had left them with a whole where their blind faith in the Clave used to be. It would've been so easy to fill it with blind resentment, but Ed had grown up a lot and he knew that it was better to fill it with this: the desire to actually do something with all that he'd learnt.

But he knew that the journey to the realisations that he'd had had been long, and that these Shadowhunters may not come to the same conclusion immediately. And that was okay; they'd accounted for that. Not everyone was going to warm to the idea of using things like alchemy to aid the cause of the Nephilim straight away.

Alec surprised him though, because the next words out of his mouth were, "I remember when we used to believe that to be the absolute truth. But sometimes the laws are simply too hard. I've seen what they can do to people; like our friend Helen Blackthorn who got sent to Wrangel Island after the Dark War simply for being half-fey. There was a time when even I feared that I would be stripped of my marks simply because I'm gay and that's not what is traditionally accepted for a Shadowhunter."

Isabelle nodded in agreement from beside her brother. "The law is hard, and that doesn't mean that you should follow it blindly. I think we all learned that the hard way."

Surprise, but not the unwelcome kind, blossomed in Ed's chest. He'd had his whole speech planned out in his head, to convince the Shadowhunters that change within the Clave could only be a good thing, but to find out that he didn't even need it was uplifting. It showed that the new generation of Shadowhunters were clearly not as stuck up and traditional as the older ones, and that perhaps they would warm to the idea of alchemy quickly. It showed that things were already changing, already morphing into something better.

"That is very true, Isabelle Lightwood," murmured Roy.

"I don't think I've ever met a stranger group of Nephilim," said Magnus, but he was smiling. "It's refreshing, if I'm honest. Nice to see how you've evolved from being stuck-up assholes."

"Magnus, we've been dating for like two years. I should hope that you'd already realised that not all of us are stuck-up assholes." Alec's voice was mock offended; it mirrored his own when he talked to Roy.

Magnus laughed a little, and took Alec's pale hand into his own. "You're an exception to any rule, Alexander."

This time it was Jace's turn to roll his eyes. "Before this conversation gets any sappier, I think we should go back to the issue at hand."

"Agreed," said Al, and though Magnus and Alec lingered a little they eventually turned away from each other's eyes and back towards the rest of the group. The love between the two men was so apparent, and seeing it made Ed smile a little. He wondered if that was how he and Roy looked to outsiders.

He hoped it was, because the pure love showing between Magnus and Alec could be described as nothing other than beautiful.

"I've got to ask, but what was your plan? You're clearly intelligent and you seem pretty determined about this whole thing." Isabelle's dark eyes were keenly curious and wicked with intelligence. Ed got the vibe that no one should ever underestimate this girl.

He shared quick glance with his brother and boyfriend before speaking. "Essentially we need to prove to the Clave first of all that alchemy isn't magic. Since it's not, and they won't tolerate as long as they think that it is, and it's also the only way the Clave will allow us back into the Shadowhunter community. That's where we need you help if possible, Magnus."

Magnus looked a little surprised. "Me? What can I do? I don't even know alchemy."

"But you do know magic. We've heard from various people that you're an extremely powerful warlock who's highly skilled in magic. We would love it if you would try and help us in finding a way to show that alchemy isn't magic by combining our knowledge with yours."

"Alone, we can't prove anything to the Clave; they simply won't listen to us. We're outcasts, so we are as important as mundanes when it comes to the affairs of the Nephilim." Al was looking at Magnus, his golden eyes laden with hope.

Magnus, however, looked relaxed; his cat eyes glancing from Ed to Al to Roy and back again. "I don't usually give help for free, except when something interests me. And you have certainly sparked my interest. I will help if I can, but I can't guarantee anything because this is something I've never done before. But I'm always up for new things."

They were the words that all three of them had been waiting to hear, the first step in their plan. They were the words that unlocked the hope within Ed. He knew that it was just the first stage, but he couldn't help that hope bubbling up within him.

"Thanks," he said, not sure what other words to use.

Al gave him a little glare. "Your help would mean the world to us, Magnus, and we'd be happy to pay."

Al had always been the more eloquent of the two brothers. Maybe Ed should let him do the speaking more often.

Under the table, Roy's hand found his, and he gave it a squeeze. Ed glanced at his boyfriend, at his dark eyes, at the smile on his face.

And the hope inside him burned a little brighter still.

* * *

Alec Lightwood had gotten used to waking up in his and Magnus's room pretty quickly after he moved in; the way the sunlight filtered in through the colourful curtains, the way there always seemed to be more pillows on the bed than the night before, the warm body sleeping next to him. It was only subtly different to waking up every morning in his room back at the Institute, but vastly much improved. Alec often woke up with a smile on his face, especially when he saw Magnus lying in the sheets, the pale sunlight kissing his skin.

This morning though, the other side of the bed was empty as Alec rolled over. He could hear voices wafting into the room from the main room of their apartment, and groaned. Magnus only ever got up before him if he had a client to look after early in the morning, and though Alec appreciated that it was Magnus's job to deal with clients, he had to admit that it was probably his least favourite thing about their lives together, especially when he wanders into the middle of a meeting to get coffee or something and is met by the distrusting eyes of a Downworlder who takes one look at his runes and curls their upper lip.

Steeling himself, Alec dragged his limbs out of the warmth of their bed and after a quick shower and pulling on some random clothes, he made his way into their living room.

Instead of a client with an unknown face, as he had been expecting, Alec was greeted with the golden eyes of the Elric brothers, who both smiled at him as he entered the room. Their 'friend' (or rather Alphonse's friend, and Edward's boyfriend), Roy Mustang was also there, but he was dressed in the black Shadowhunter gear, a contrast to the Elrics' jeans and shirts.

"Ah, Alexander," said Magnus, making his way over to Alec and kissing him lightly on the lips. Alec was keenly aware of his cheeks turning rosy; he still wasn't completely used to casual displays of affection in front of other people despite the years; he probably wouldn't ever be if he was honest.

"Morning," he mumbled, causing Magnus to grin at him. "I didn't know you would be here today," he said, this time addressing the three guests.

Edward shrugged. "We figured that we may as well start trying to figure all this out. It's probably gonna take a while; there are an lot of nuances in alchemy and I'm assuming the same for magic, and we need to work out how they contrast, and also a way to easily show how they contrast to someone who has no idea about either of them."

Ed's voice held tones of excitement lurking beneath it, and Alec couldn't blame him. This was his chance at getting back his honour and standing in the Clave, but also his chance to change the society that he had come to despise for the better. If he was in their situation, he would be excited too.

"That's where you come in, Alexander. We'll need to test some of our explanations and theories in front of someone who's essentially clueless about both alchemy and magic, and you're my first choice." Magnus was grinning at him falsely, and Alec rolled his eyes.

"I'm not sure whether to take that as a compliment or an insult, but judging by the look on your face, probably the latter."

"Hey, I'm not saying you're stupid. Just currently uneducated about these certain aspects, but luckily we need someone uneducated about these things. Your help will be essential, of course."

He found himself nodding, muttering "yeah, yeah, whatever," under his breath, which caused Magnus to grin at him.

The conversation then quickly descended into something that went right over Alec's head, about transmutation circles versus summoning circles or something equally as confusing, so he went to get himself a coffee and something to eat.

Unexpectedly, someone followed him into the kitchen: Roy Mustang stood looking at him with dark eyes and an unreadable expression on his face.

Alec leant back on the counter, unsure as to why he had trailed him into the room. "You look ready to throw yourself into battle. Bit of a contrast to the first outfit we saw you in." Looking back on it, seeing a grown man burst into the room in his pyjamas would've been hilarious if it weren't for the circumstances, and Alec was graced with a smile from Roy at the memory.

"Yeah, I must admit that whilst I was the height of fashion, I'm sure that the Clave members wouldn't appreciate me bursting back into Alicante in my pyjamas. I think that gear is probably more suitable."

"You're leaving?" He couldn't keep the surprise out of his voice; for some reason he had expected Roy to stay with the Elrics as they worked with Magnus.

Roy simply nodded. "Duty calls. I can only stay away from Idris for so long before it begins to look suspicious. I'm still setting myself up as an important Clave member, perhaps even Consul if the opportunity ever arises again, and I can't have long leaves of absence. My parabatai Riza said she would cover for me this time since it was an emergency, but I should've probably left days ago."

There was a deep sadness that echoed in Roy's voice, and Alec knew that he was thinking of Edward and the prospect of leaving him again. He couldn't imagine not being able to live with Magnus now, not being allowed to see his face or kiss his lips every day.

"I'm sorry that you have to leave him," Alec murmured. "No one should have to spend time away from the person they love most in the world."

The older man looked a little startled at Alec's words, but then smiled to himself. "Am I that obvious? That I'm in love with Fullmet—with Ed?"

Alec smiled, a genuine smile as he recalled the expressions Roy and Ed shared, and how utterly similar they were to the ones he and Magnus exchanged. "You both are. It's kinda cute, actually."

Roy scratched the back of his neck. "It's all still pretty new. I mean, I've known him for years, but the whole relationship thing is still new to me, I guess. And we have barely any opportunity to spend time together."

"I'm sorry, it must be hard. I really hope that the two of them manage to figure this out, so you can see him more." Alec meant the words he was saying, both because he wanted the Elrics to succeed and perhaps introduce alchemy into the society of Nephilim because it was a great idea, but also because Edward and Alphonse both deserved a chance to be happy and be with the people they loved, like Roy. They had saved the world, for Angel's sake.

"It's fine. I'm sure that good will eventually come of it and I won't have to sneak out of Idris just to see him. But I am kinda doing this for them, trying to get high up within the Clave. As much as it has always been my ambition to bring about change in the Clave, I also just want to help them from the inside. If I ever became Consul, the first thing I would do is allow them back into Idris, back to their home. They don't deserve to be exiles any more than you or your friends. But in order to do that, we have to make sacrifices."

Sacrifices were a familiar subject for Alec; he'd made enough and had seen many others around him make them too.

Roy glanced at Alec, and then continued. "You know, I was there in Idris when you kissed Magnus before the Mortal War. I've always admired your courage for doing that; knowing the Clave and their ridiculous traditional values. Coming out like that was an amazing thing to do."

Although he's been told similar things before, it still made Alec blush a little. He had only been thinking of Magnus and what he'd said and how much he'd needed to show Magnus that he loved him, and not really what the consequences of his actions would be. "It was nothing really. In an ideal world, it wouldn't have been a big deal at all."

"Of course…Obviously, I have to keep my relationship with Edward a secret for the moment; revealing that I'm dating a male fugitive from the Clave who's six years my junior wouldn't help me climb the ranks of the Council. But when I saw you here and I remembered that day in Idris, it made me wish that I could be open like that. But someday, I'd like to boast about how amazing Ed is, and how much he means to me, without feeling like I have to keep him as some sort of dirty secret."

Alec was reminded of the days when he thought that keeping his relationship with Magnus a secret was the right thing to do. In the end, coming clean about it was probably one of the best things he ever did; it transformed his life for the better. He hoped that Roy and Edward would be able to do it too, even though the circumstances were tricky.

"It's difficult, I get it. It's not like it was an easy ride to declare that I was dating a male warlock, and I'm almost positive that most of the Council doesn't approve of it." He paused and looked at Roy. He looked like a typical Shadowhunter standing there in his gear, runes peeking out from under his clothes, seraph blades at his belt. A warrior completely manufactured by the Clave. Yet here he was with his illicit boyfriend, planning on helping him revolutionise the Clave.

Not everyone was what they seemed, Alec thought with a smile.

At that moment, Magnus poked his head into the kitchen. "Sorry about this, Roy, but your Portal back to Idris is ready."

They exited the kitchen and went back into the living room, where Alphonse was sat on the couch and Edward stood next to the Portal that had materialised from Magnus's fingertips. Alec could see the green fields of Idris through it, a manor house in the distance. Edward was staring at it intensely, and Alec realised with a jolt that he probably hadn't seen Idris any closer than this in years, despite having grown up there. It must be painful, having your home so tantalisingly close but not being able to set foot there.

"Fullmetal," Roy said softly, and Edward turned to him, his golden eyes unreadable.

Alec felt a little awkward as Roy and Edward embraced, their lips finding each other as they said goodbye. Public displays of affection were all well and good if you were a part of them but now Alec wasn't sure where to look.

When the pair broke apart, they mumbled a few things to each other that Alec couldn't make out, and then turned back to the rest of the group. Their hands were still entwined.

"Say hi to Winry for us," said Alphonse "She knows that we're terrible at calling, and it's been a surprisingly long amount of time since Brother broke his automail so we've not seen her in far too long."

Roy's mouth quirked up in a smile. "I will, but you should call her more often; I know she worries. But if you're staying in New York for a while, I'll tell her to visit."

Roy gave a little wave, which Alphonse reciprocated, and then leant back to kiss Edward one last time. "See you soon, yeah, Bastard? Maybe next time we meet it will be in the Glass City." Ed's voice was quiet but clear, and Alec could hear the steely determination behind it.

Roy Mustang took one last look and then stepped through the Portal. The air around it shimmered, and then it glowed blue and disappeared as Magnus clicked his fingers. Edward let out a breath, and sat down on the couch with his brother.

Magnus glanced at him, his green-yellow eyes conveying an unspoken message. Alec knew his boyfriend well enough by now that he could see that he was all the more motivated to help these two brothers now. He was sure that Magnus was thinking the same things as he had been in the kitchen, about how undeserving Edward and Alphonse were of their punishment. About how Edward and Roy deserved the chance to be together the way the two of them had been.

"Not to be annoying, but could we carry on trying to figure this out?" Alec could see that they had always been leading up to this moment of finally beginning to figure out how they can convince the Clave of their alchemy. This was their shot at doing what they had been building up to, at going home.

Magnus smiled. "Of course."

The conversation once again quickly drifted to alchemy and magic, and though Alec was lost virtually immediately he sat down and let it wash over him. He sat there thinking about what he could learn from the Elrics, about their story and where it was going to take them.

He couldn't help but admire them, as they started this journey that could lead to such huge changes for all of them. The two bothers may finally be able to return home, and though knowing the Clave they would never truly receive the recognition they deserved, they would be able to make a difference if they managed to do this right. Alchemy was their undoing but also clearly something they loved so much, and even though he hadn't known them a long time, Alec knew that they were the kind of stubborn people who weren't going to give up on something that they were passionate about. He could see it in their eyes, those flames of determination behind those golden irises.

Alec had nothing but hope for the Elrics, as he sat there watching them talk about equivalent exchange and philosopher's stones. It was almost mesmerising, and certainly inspirational, to see their single-mindedness. Despite Ed's constant reminder of the scientific nature of alchemy, he couldn't help but muse that even if the alchemy wasn't magic, maybe the Elrics still had some magic in them. Maybe this fire and hope and passion was their own form of magic.

* * *

 **A/N: find me on tumblr at alecliqhtwood and twitter at alchemyhowell :)**


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